rs201439705
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_000232.5(SGCB):c.392G>T(p.Arg131Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000186 in 1,613,586 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
SGCB
NM_000232.5 missense
NM_000232.5 missense
Scores
14
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.80
Genes affected
SGCB (HGNC:10806): (sarcoglycan beta) This gene encodes a member of the sarcoglycan family. Sarcoglycans are transmembrane components in the dystrophin-glycoprotein complex which help stabilize the muscle fiber membranes and link the muscle cytoskeleton to the extracellular matrix. Mutations in this gene have been associated with limb-girdle muscular dystrophy.[provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM1
In a topological_domain Extracellular (size 231) in uniprot entity SGCB_HUMAN there are 44 pathogenic changes around while only 2 benign (96%) in NM_000232.5
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SGCB | NM_000232.5 | c.392G>T | p.Arg131Leu | missense_variant | 3/6 | ENST00000381431.10 | NP_000223.1 | |
SGCB | XM_047416074.1 | c.182G>T | p.Arg61Leu | missense_variant | 2/5 | XP_047272030.1 | ||
SGCB | XM_047416075.1 | c.95G>T | p.Arg32Leu | missense_variant | 2/5 | XP_047272031.1 | ||
SGCB | XM_047416076.1 | c.95G>T | p.Arg32Leu | missense_variant | 2/5 | XP_047272032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SGCB | ENST00000381431.10 | c.392G>T | p.Arg131Leu | missense_variant | 3/6 | 1 | NM_000232.5 | ENSP00000370839.6 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151984Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461602Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727104
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151984Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74230
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
D
MutationAssessor
Benign
L
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Loss of catalytic residue at R131 (P = 0.041);
MVP
MPC
ClinPred
D
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at